Align fructose-bisphosphate aldolase class II; EC 4.1.2.13 (characterized)
to candidate 17004 b2925 fructose-bisphosphate aldolase (NCBI)
Query= CharProtDB::CH_024118 (359 letters) >FitnessBrowser__Keio:17004 Length = 359 Score = 728 bits (1879), Expect = 0.0 Identities = 359/359 (100%), Positives = 359/359 (100%) Query: 1 MSKIFDFVKPGVITGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQ 60 MSKIFDFVKPGVITGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQ Sbjct: 1 MSKIFDFVKPGVITGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQ 60 Query: 61 FSNGGASFIAGKGVKSDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWI 120 FSNGGASFIAGKGVKSDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWI Sbjct: 61 FSNGGASFIAGKGVKSDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWI 120 Query: 121 DGLLDAGEKHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKIGMTLEIELGCTG 180 DGLLDAGEKHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKIGMTLEIELGCTG Sbjct: 121 DGLLDAGEKHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKIGMTLEIELGCTG 180 Query: 181 GEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPT 240 GEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPT Sbjct: 181 GEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPT 240 Query: 241 ILRDSQEYVSKKHNLPHNSLNFVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWATWEGV 300 ILRDSQEYVSKKHNLPHNSLNFVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWATWEGV Sbjct: 241 ILRDSQEYVSKKHNLPHNSLNFVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWATWEGV 300 Query: 301 LNYYKANEAYLQGQLGNPKGEDQPNKKYYDPRVWLRAGQTSMIARLEKAFQELNAIDVL 359 LNYYKANEAYLQGQLGNPKGEDQPNKKYYDPRVWLRAGQTSMIARLEKAFQELNAIDVL Sbjct: 301 LNYYKANEAYLQGQLGNPKGEDQPNKKYYDPRVWLRAGQTSMIARLEKAFQELNAIDVL 359 Lambda K H 0.316 0.133 0.392 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 623 Number of extensions: 5 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 359 Length of database: 359 Length adjustment: 29 Effective length of query: 330 Effective length of database: 330 Effective search space: 108900 Effective search space used: 108900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
Align candidate 17004 b2925 (fructose-bisphosphate aldolase (NCBI))
to HMM TIGR01520 (fbaA: fructose-bisphosphate aldolase, class II (EC 4.1.2.13))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR01520.hmm # target sequence database: /tmp/gapView.7811.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01520 [M=357] Accession: TIGR01520 Description: FruBisAldo_II_A: fructose-bisphosphate aldolase, class II Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-197 642.0 0.4 1.4e-197 641.8 0.4 1.0 1 lcl|FitnessBrowser__Keio:17004 b2925 fructose-bisphosphate aldo Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:17004 b2925 fructose-bisphosphate aldolase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 641.8 0.4 1.4e-197 1.4e-197 1 356 [. 4 358 .. 4 359 .] 0.99 Alignments for each domain: == domain 1 score: 641.8 bits; conditional E-value: 1.4e-197 TIGR01520 1 vldklktgvilgedvaklfevakeekfaiPainvvssetvnaaleaardakspiilqfsnggaafiaGkGvkdeaekaa 79 ++d++k+gvi+g+dv+k+f+vake++fa+Pa+n+v+++++na+le+a+++k+p+i+qfsngga+fiaGkGvk++++++a lcl|FitnessBrowser__Keio:17004 4 IFDFVKPGVITGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQFSNGGASFIAGKGVKSDVPQGA 82 6899*************************************************************************** PP TIGR01520 80 siaGaiaaaeyvrsiaekygvpvvlhtdhCakkllpyvdglleadekyfkkegkPlfsshmldlseepieenieiakky 158 +i Gai++a++v+++ae+ygvpv+lhtdhCakkllp++dgll+a+ek+f+++gkPlfsshm+dlsee+++eniei++ky lcl|FitnessBrowser__Keio:17004 83 AILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWIDGLLDAGEKHFAATGKPLFSSHMIDLSEESLQENIEICSKY 161 ******************************************************************************* PP TIGR01520 159 lkrmakiklileieiGitGGeedGvdneeadkeelytkPedvekvyeelskispkfsiaaafGnvhGvykpGnvklrPd 237 l+rm+ki ++leie+G+tGGeedGvdn+++d+++lyt+Pedv+++y+elskisp+f+iaa+fGnvhGvykpGnv+l+P+ lcl|FitnessBrowser__Keio:17004 162 LERMSKIGMTLEIELGCTGGEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPT 240 ******************************************************************************* PP TIGR01520 238 iladgqeyvaeklglkeakplsfvfhGGsGstkeeikealsyGvvkvnvdtdtqyaalegildyvlknedylqsqvGnp 316 il+d+qeyv++k++l+ +++l+fvfhGGsGst++eik+++syGvvk+n+dtdtq+a++eg+l+y+++ne+ylq+q+Gnp lcl|FitnessBrowser__Keio:17004 241 ILRDSQEYVSKKHNLP-HNSLNFVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWATWEGVLNYYKANEAYLQGQLGNP 318 ****************.9************************************************************* PP TIGR01520 317 kgeekpnkkvydPrvwlreaeksmkarvekaleelnaink 356 kge++pnkk+ydPrvwlr++++sm+ar+eka++elnai++ lcl|FitnessBrowser__Keio:17004 319 KGEDQPNKKYYDPRVWLRAGQTSMIARLEKAFQELNAIDV 358 *************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (357 nodes) Target sequences: 1 (359 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.70 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory